They heavily recommend to use your own server as an intermediary for validation, as this will allow a clear and secure passage to the App Store for all versions of iOS. That's really the best route to not be damned either way.
If you must perform validation directly from the device to the App Store, then you utilise their mitigation strategy only when the application is run on 5.1.x and below. For iOS6 and above, use the recommended means provided.
Whilst it was always the case that you shouldn't parse the receipt directly, the discovered vulnerability put Apple between a rock and a hard place in how to address this, and decided that application developers implement a check. It means when a user updates the application, the receipts are now secured again (irrespective of iOS version), thereby providing better fix coverage. As a side effect, it means you have to break from how you should normally do it (but Apple have give you permission to do so).
I agree the documentation isn't wholly clear on this, and could be clarified a bit more (you should give them feedback from the documentation pages at the bottom). Apple have published a mitigation strategy, and they do state it should be used on iOS 5.1.x and below to address the vulnerability. The onus is on them if they change the format/contents of IAP receipts.